Until and unless DC starts publishing a Superboy
title, with the adventures of Superman when he was a boy, I view the point from which he was born through the time he became Superman as tied to his origin. So, whether it's his time on Krypton or in Smallville, it's all the same to me.
And, honestly, unless DC does plan on telling more stories past this mini-series about Clark's life in Smallville, I don't see the point in adding Chloe, because I don't believe she has a role in the adult Superman's life, other than to become just another of the long list of secondary characters which are largely ignored. In his past, she could be the stand in for Lois, the one who doesn't know his secret identity (assuming the MoS
origin where he tells Lana holds true).
DC's only just brought Cat Grant, Ron Troupe, and Steve Lombard back from relative limbo (Cat and Ron having spent less time there than Steve). Bibbo and the Guardian are back also, but since "New Krypton" ended, we've not see the staff of the Daily Planet at all. Where would Chloe fit into that? Or should she be included in Geoff's story, reference once in a while, but not added to the regular cast?